Why do I have left-over tonnage when I make a build in-game?
Many mechs in-game have armor quirks, which give 'free armor' that doesn't weigh anything, in addition to the expected amount of armor a mech should have (for example: Annihilator, King Crab, Atlas). Smurfy doesn't take this into account. If you build your mech using Smurfy's armor values, you will end up with left-over tonnage because you removed more armor in comparison to the maximum value.
In order to fix this, go for a fully armored mech and only then remove armor in the same way it's removed from smurfy (example: 43/56 armor on a location means 56-43 = 13 armor taken away). Take note that many builders don't redistribute armor for the reason that it's inaccurate anyway. Figure out your own preferred front/back armor ratios.
In the other 10% of the time, if fixing the armor doesn't solve your issue, double-check if you're missing ammo, or using the right engine, for example.